Setup

Load R libraries

library(data.table)
library(ggplot2)
library(ggpubr)
library(tidyr)
library(limma)
library(stringr)

theme_set(theme_classic())

cell_type_name = params$cell_type_name
graph_weight = params$graph_weight

cell_type_name
## [1] "cd8"
graph_weight
## [1] "2.0"

Check enrichment of gene sets

Read in gene info and gene set assignments

file_tag = sprintf("%s_BL_%s", cell_type_name, graph_weight)

assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag), 
                     what = character(), sep="\n")

gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag), 
                 what = character(), sep="\n")

gene_sets = sapply(gene_sets, strsplit, USE.NAMES=FALSE, split=",")
n_genes   = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   16.00   17.00   18.00   17.85   18.00   19.00
length(n_genes)
## [1] 40
sort(n_genes)
##  [1] 16 17 17 17 17 17 17 17 17 17 17 17 18 18 18 18 18 18 18 18 18 18 18 18 18
## [26] 18 18 18 18 18 18 18 18 19 19 19 19 19 19 19

Find gene symbols using the alias2Symbol function from limma.

a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
  gi = assayed_genes[i]
  ai = alias2Symbol(gi)
  if(length(ai) > 1){
    print(gi)
    print(ai)
  }
  a2s[i] = ai[1]
}
## [1] "QARS"
## [1] "EPRS1" "QARS1"
## [1] "SEPT2"
## [1] "SEPTIN6" "SEPTIN2"
table(is.na(a2s))
## 
## FALSE  TRUE 
##  1607    42
table(a2s == assayed_genes, useNA = 'ifany')
## 
## FALSE  TRUE  <NA> 
##    42  1565    42
gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)

gene_info[sym_in_data != sym_limma,]
##     sym_in_data sym_limma
##  1:    C10orf91 LINC02870
##  2:    C12orf10      MYG1
##  3:    C12orf45  NOPCHAP1
##  4:     C6orf48    SNHG32
##  5:     C6orf99 LINC02901
##  6:    CXorf40A     EOLA1
##  7:     CXorf57      RADX
##  8:     FAM102A     EEIG1
##  9:     FAM173A    ANTKMT
## 10:     FAM213B    PRXL2B
## 11:       H2AFX      H2AX
## 12:   HIST1H2AG    H2AC11
## 13:   HIST1H2BK    H2BC12
## 14:   HIST1H2BN    H2BC15
## 15:    HIST1H3A      H3C1
## 16:    HIST1H3H     H3C10
## 17:    HIST1H4C      H4C3
## 18:   HIST2H2BF    H2BC18
## 19:    KIAA0391     PRORP
## 20:        QARS     EPRS1
## 21:       SEPT6   SEPTIN6
## 22:       ARNTL     BMAL1
## 23:    C12orf65     MTRFR
## 24:    C16orf72   HAPSTR1
## 25:      CCDC84   CENATAC
## 26:      DOPEY2     DOP1B
## 27:     FAM126B     HYCC2
## 28:    FAM160B1    FHIP2A
## 29:        H1FX     H1-10
## 30:       H2AFJ      H2AJ
## 31:       HEXDC      HEXD
## 32:    HIST1H1C      H1-2
## 33:    HIST1H1D      H1-3
## 34:    HIST1H1E      H1-4
## 35:    KIAA1109     BLTP1
## 36:    KIAA1551     RESF1
## 37:        MKL1     MRTFA
## 38:       NARFL     CIAO3
## 39:       SEPT2   SEPTIN6
## 40:      TARSL2     TARS3
## 41:      TMEM8A     PGAP6
## 42:       WDR60   DYNC2I1
##     sym_in_data sym_limma
gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")), 
                gene_symbol := sym_limma]

dim(gene_info)
## [1] 1649    3
gene_info[1:5,]
##    sym_in_data sym_limma gene_symbol
## 1:      ABLIM1    ABLIM1      ABLIM1
## 2:  AC004687.1      <NA>  AC004687.1
## 3:  AC004854.2      <NA>  AC004854.2
## 4:  AC007384.1      <NA>  AC007384.1
## 5:  AC007952.4      <NA>  AC007952.4
t1 = table(gene_info$gene_symbol)
table(t1)
## t1
##    1    2 
## 1647    1
gene_info[gene_symbol %in% names(t1)[t1 == 2],]
##    sym_in_data sym_limma gene_symbol
## 1:       SEPT6   SEPTIN6     SEPTIN6
## 2:       SEPT2   SEPTIN6     SEPTIN6
gene_info[sym_in_data == "HIST1H2BC", gene_symbol:="H2BC4"]
gene_info[sym_in_data == "HIST1H2BG", gene_symbol:="H2BC8"]
gene_info[sym_in_data == "SEPT6", gene_symbol:="SEPTIN6"]
gene_info[sym_in_data == "SEPT2", gene_symbol:="SEPTIN2"]

Read in cell type-specific expression data

Cell type specific gene expression were downloaded from protein atlas.

ct = fread("../Annotation/rna_single_cell_type.tsv.gz")
dim(ct)
## [1] 1587110       4
ct[1:5,]
##               Gene Gene name             Cell type  nTPM
## 1: ENSG00000000003    TSPAN6            Adipocytes 149.5
## 2: ENSG00000000003    TSPAN6 Alveolar cells type 1   6.1
## 3: ENSG00000000003    TSPAN6 Alveolar cells type 2  10.5
## 4: ENSG00000000003    TSPAN6            Astrocytes  13.9
## 5: ENSG00000000003    TSPAN6               B-cells   1.5
length(unique(ct$`Cell type`))
## [1] 79
table(ct$`Cell type`)
## 
##                      Adipocytes           Alveolar cells type 1 
##                           20090                           20090 
##           Alveolar cells type 2                      Astrocytes 
##                           20090                           20090 
##                         B-cells             Basal keratinocytes 
##                           20090                           20090 
##           Basal prostatic cells         Basal respiratory cells 
##                           20090                           20090 
## Basal squamous epithelial cells                   Bipolar cells 
##                           20090                           20090 
##          Breast glandular cells      Breast myoepithelial cells 
##                           20090                           20090 
##                  Cardiomyocytes                  Cholangiocytes 
##                           20090                           20090 
##                      Club cells           Collecting duct cells 
##                           20090                           20090 
##        Cone photoreceptor cells                Cytotrophoblasts 
##                           20090                           20090 
##                 dendritic cells              Distal enterocytes 
##                           20090                           20090 
##            Distal tubular cells                    Ductal cells 
##                           20090                           20090 
##                Early spermatids      Endometrial ciliated cells 
##                           20090                           20090 
##       Endometrial stromal cells               Endothelial cells 
##                           20090                           20090 
##           Enteroendocrine cells                 Erythroid cells 
##                           20090                           20090 
##              Excitatory neurons        Exocrine glandular cells 
##                           20090                           20090 
##       Extravillous trophoblasts                     Fibroblasts 
##                           20090                           20090 
##   Gastric mucus-secreting cells     Glandular and luminal cells 
##                           20090                           20090 
##                    granulocytes                 Granulosa cells 
##                           20090                           20090 
##                     Hepatocytes                  Hofbauer cells 
##                           20090                           20090 
##                Horizontal cells              Inhibitory neurons 
##                           20090                           20090 
##         Intestinal goblet cells                       Ionocytes 
##                           20090                           20090 
##                   Kupffer cells                Langerhans cells 
##                           20090                           20090 
##                 Late spermatids                    Leydig cells 
##                           20090                           20090 
##                     Macrophages                     Melanocytes 
##                           20090                           20090 
##                Microglial cells                       monocytes 
##                           20090                           20090 
##           Mucus glandular cells               Muller glia cells 
##                           20090                           20090 
##                        NK-cells Oligodendrocyte precursor cells 
##                           20090                           20090 
##                Oligodendrocytes      Pancreatic endocrine cells 
##                           20090                           20090 
##                    Paneth cells               Peritubular cells 
##                           20090                           20090 
##                    Plasma cells       Prostatic glandular cells 
##                           20090                           20090 
##            Proximal enterocytes          Proximal tubular cells 
##                           20090                           20090 
##      Respiratory ciliated cells         Rod photoreceptor cells 
##                           20090                           20090 
##             Salivary duct cells                   Schwann cells 
##                           20090                           20090 
##          Serous glandular cells                   Sertoli cells 
##                           20090                           20090 
##               Skeletal myocytes             Smooth muscle cells 
##                           20090                           20090 
##                   Spermatocytes                   Spermatogonia 
##                           20090                           20090 
##       Squamous epithelial cells        Suprabasal keratinocytes 
##                           20090                           20090 
##            Syncytiotrophoblasts                         T-cells 
##                           20090                           20090 
##                     Theca cells         Thymic epithelial cells 
##                           20090                           20090 
##          Undifferentiated cells 
##                           20090
ct_immune = fread("../Annotation/rna_immune_cell_monaco.tsv.gz")
dim(ct_immune)
## [1] 602700      5
ct_immune[1:5,]
##               Gene Gene name                Immune cell TPM pTPM
## 1: ENSG00000000003    TSPAN6                   basophil  NA  1.2
## 2: ENSG00000000003    TSPAN6  Central memory CD8 T-cell  NA  1.7
## 3: ENSG00000000003    TSPAN6         classical monocyte  NA  0.2
## 4: ENSG00000000003    TSPAN6 Effector memory CD8 T-cell  NA  0.7
## 5: ENSG00000000003    TSPAN6    Exhausted memory B-cell  NA  0.7
summary(ct_immune$TPM)
##    Mode    NA's 
## logical  602700
summary(ct_immune$pTPM)
##     Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
##     0.00     0.00     3.10    49.74    27.20 96572.50
summary(ct_immune$pTPM[ct_immune$pTPM > 0])
##     Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
##     0.10     1.70    11.60    67.96    42.80 96572.50
length(unique(ct_immune$`Immune cell`))
## [1] 30
table(ct_immune$`Immune cell`)
## 
##                            basophil           Central memory CD8 T-cell 
##                               20090                               20090 
##                  classical monocyte          Effector memory CD8 T-cell 
##                               20090                               20090 
##             Exhausted memory B-cell               intermediate monocyte 
##                               20090                               20090 
##                         MAIT T-cell               Memory CD4 T-cell TFH 
##                               20090                               20090 
##               Memory CD4 T-cell Th1          Memory CD4 T-cell Th1/Th17 
##                               20090                               20090 
##              Memory CD4 T-cell Th17               Memory CD4 T-cell Th2 
##                               20090                               20090 
##                          myeloid DC                        naive B-cell 
##                               20090                               20090 
##                    naive CD4 T-cell                    naive CD8 T-cell 
##                               20090                               20090 
##                          neutrophil                             NK-cell 
##                               20090                               20090 
##              non-classical monocyte          Non-switched memory B-cell 
##                               20090                               20090 
##                       Non-Vd2 gdTCR                         Plasmablast 
##                               20090                               20090 
##                     plasmacytoid DC                     Progenitor cell 
##                               20090                               20090 
##              Switched memory B-cell                               T-reg 
##                               20090                               20090 
## Terminal effector memory CD4 T-cell Terminal effector memory CD8 T-cell 
##                               20090                               20090 
##                          total PBMC                           Vd2 gdTCR 
##                               20090                               20090
lineage = fread("../Annotation/rna_immune_cell_monaco_cell_types.tsv")
dim(lineage)
## [1] 30  2
lineage[1:2,]
##     Cell_type      Lineage
## 1:   Basophil Granulocytes
## 2: Neutrophil Granulocytes

Check gene expression for each gene set

dim(gene_info)
## [1] 1649    3
for(k in 1:length(gene_sets)){
  if(length(gene_sets[[k]]) < 10) { next }
  
  print(k)
  set_k = paste0("set_", k)
  print(gene_sets[[k]])
  
  genes = gene_info[sym_in_data %in% gene_sets[[k]], gene_symbol]

  n_genes = sum(genes %in% ct_immune$`Gene name`)
  print(sprintf("found %d genes.", n_genes))

  if(n_genes == 0) { next }

  df = ct_immune[`Gene name` %in% genes,]
  dim(df)
  df[1:2,]
  
  stopifnot(all(str_to_lower(df$`Immune cell`) %in% 
                  str_to_lower(lineage$Cell_type)))
  
  mat1 = match(str_to_lower(df$`Immune cell`), 
               str_to_lower(lineage$Cell_type))
  
  df = cbind(df, lineage[mat1,])
  df[1:2,]
  
  df$Cell_type = factor(df$Cell_type, levels = lineage$Cell_type)
  df = df[df$Lineage != "Total PBMC",]
  df$Lineage   = factor(df$Lineage, 
                        levels = setdiff(lineage$Lineage, "Total PBMC"))
  
  p1 = ggplot(df, aes(x=Cell_type, y=log10(pTPM + 0.1), fill=Lineage)) + 
    geom_boxplot() + xlab("Cell type") + ggtitle(set_k) + 
    theme(axis.text.x = element_text(angle = 45, hjust = 1)) + 
    scale_fill_brewer(palette="RdBu")

  print(p1)
}
## [1] 1
##  [1] "ARHGEF3"   "ARL4C"     "BROX"      "COL6A2"    "COL6A3"    "DMTF1"    
##  [7] "ELMOD3"    "FAM169A"   "GPR174"    "IFITM2"    "LAIR2"     "LINC02256"
## [13] "PIK3CD"    "PIK3R5"    "RUBCN"     "SLCO3A1"   "SUSD6"     "TRGV10"   
## [19] "XCL1"     
## [1] "found 18 genes."

## [1] 2
##  [1] "ISCA1"    "LCP2"     "NSUN6"    "NT5E"     "SLC27A5"  "TRAT1"   
##  [7] "AFF1"     "AFF4"     "COX19"    "ITK"      "LONP2"    "MYO9A"   
## [13] "PNPLA8"   "TBC1D14"  "TRAPPC11" "TRAPPC8"  "TRAPPC9"  "ZNF557"  
## [1] "found 18 genes."

## [1] 3
##  [1] "CAMK4"    "CCNB1IP1" "CMTM7"    "EPHX2"    "HDHD3"    "HIBADH"  
##  [7] "LBH"      "MZT2A"    "PCMTD2"   "PDE7A"    "SNHG15"   "TC2N"    
## [13] "THEM4"    "ZFAS1"    "CD46"     "FAM126B"  "KLF3"     "VPS13A"  
## [1] "found 15 genes."

## [1] 4
##  [1] "CREBL2"   "DYRK4"    "IGKV3-20" "MZF1"     "NBPF14"   "TBCCD1"  
##  [7] "TRAV13-1" "TRAV8-3"  "TRGV5"    "TSPYL4"   "CYTOR"    "IQCG"    
## [13] "PATL2"    "PYROXD1"  "SENP7"    "TRIM38"   "TSPAN32"  "ZNF683"  
## [1] "found 17 genes."

## [1] 5
##  [1] "CCR7"       "TRABD2A"    "AC116407.2" "DOCK10"     "HRH2"      
##  [6] "LINC02446"  "MX2"        "OAS2"       "OXNAD1"     "PCED1B"    
## [11] "S100A12"    "TRAV12-3"   "TRAV19"     "TRAV27"     "TRAV4"     
## [16] "TRAV9-2"    "TRBV11-2"   "TRBV4-2"   
## [1] "found 15 genes."

## [1] 6
##  [1] "BBS9"     "COG5"     "DTHD1"    "KLRF1"    "LRRC23"   "MAP3K2"  
##  [7] "MTRNR2L8" "NT5C3B"   "TOX"      "TRAV3"    "TRBV7-2"  "TRGV8"   
## [13] "ZNF862"   "COG7"     "MCTP2"    "MYBL1"    "TRGC2"   
## [1] "found 17 genes."

## [1] 7
##  [1] "CST3"    "APOL6"   "CD226"   "DIAPH2"  "DOCK11"  "EPSTI1"  "ERAP2"  
##  [8] "GNPTAB"  "GPR141"  "LILRB1"  "MIGA1"   "OGA"     "PARP15"  "PTPRJ"  
## [15] "ST6GAL1" "TTC17"   "UNC13D"  "ZNF493" 
## [1] "found 18 genes."

## [1] 8
##  [1] "ARMH1"     "BTG1"      "IL6R"      "SLC2A3"    "TMIGD2"    "ARHGAP45" 
##  [7] "DDIT4"     "HEXDC"     "IL6ST"     "ITM2A"     "OSM"       "PPP4R3B"  
## [13] "PSMA3-AS1" "STK17B"    "TARSL2"    "TENT5C"    "Z93930.2"  "ZC3H7B"   
## [1] "found 16 genes."

## [1] 9
##  [1] "ALOX5AP"  "FCRL3"    "GCSAM"    "GTF3A"    "ICAM3"    "MFNG"    
##  [7] "TRBC1"    "ADGRE5"   "ARHGAP30" "CCL4"     "CD38"     "CTSW"    
## [13] "FCRL6"    "FGFBP2"   "SLA2"     "TBC1D2B"  "TRBC2"    "ZAP70"   
## [19] "ZNF276"  
## [1] "found 19 genes."

## [1] 10
##  [1] "ANKRD49"  "ATAD2B"   "CCNH"     "CES1"     "CLUH"     "FAM13B"  
##  [7] "GPATCH2L" "INO80D"   "MICAL2"   "MX1"      "NAA25"    "NARFL"   
## [13] "NLRC5"    "PARP9"    "RHOH"     "STAT4"    "SYNRG"   
## [1] "found 17 genes."

## [1] 11
##  [1] "AC027644.3" "AC087623.3" "AC119396.1" "AC245297.3" "ARRDC2"    
##  [6] "IER5"       "KLF10"      "KMT2E-AS1"  "LINC00649"  "RAB33B"    
## [11] "SDR42E2"    "SESN2"      "TCP11L2"    "WARS2"      "MARF1"     
## [16] "RUFY2"      "SZT2"       "XIST"      
## [1] "found 11 genes."

## [1] 12
##  [1] "ASL"     "GALNT11" "NXT2"    "ASCL2"   "BTN3A1"  "FRYL"    "GNLY"   
##  [8] "GON4L"   "HSH2D"   "INPP4A"  "PHF14"   "POLH"    "RALGAPB" "SEMA4D" 
## [15] "TAOK1"   "TAOK3"   "USP16"   "ZEB2"   
## [1] "found 18 genes."

## [1] 13
##  [1] "AL118516.1"  "AL451085.1"  "AL627171.1"  "ATP2B1-AS1"  "HELQ"       
##  [6] "INPP4B"      "LINC02273"   "NUP58"       "PRR7"        "PTGER4"     
## [11] "RGS1"        "AC016831.7"  "CEMIP2"      "CRYBG1"      "GDPD5"      
## [16] "PRR5L"       "THUMPD3-AS1" "TMEM131L"   
## [1] "found 11 genes."

## [1] 14
##  [1] "RELT"      "B4GALT1"   "CAPNS1"    "CROCC"     "CST7"      "CX3CR1"   
##  [7] "DDHD1"     "IL2RG"     "IRAK4"     "LINC02384" "MBP"       "RNF213"   
## [13] "SAMD9L"    "SPN"       "SYNE1"     "UBE2H"     "UBR2"     
## [1] "found 16 genes."

## [1] 15
##  [1] "CYB5D2"  "INTS6"   "INTS8"   "PASK"    "PITPNC1" "TMEM134" "TRG-AS1"
##  [8] "CCDC88C" "EFHD2"   "GZMA"    "GZMH"    "NEAT1"   "PEX1"    "PEX26"  
## [15] "PRR14L"  "SSH1"    "STK10"  
## [1] "found 15 genes."

## [1] 16
##  [1] "AC004854.2" "AC083798.2" "AK5"        "CD40LG"     "CITED2"    
##  [6] "EI24"       "FAM213B"    "FXYD7"      "MYLIP"      "NR1D1"     
## [11] "PIK3IP1"    "PPP1R15B"   "RGL4"       "SLC38A2"    "TESPA1"    
## [16] "WDR86"      "WSB1"       "ARRDC3"     "ITPR2"     
## [1] "found 17 genes."

## [1] 17
##  [1] "ABCA5"      "AC020659.1" "ADHFE1"     "CCDC84"     "CLEC16A"   
##  [6] "CPPED1"     "DDX60L"     "GABPB2"     "GCN1"       "HECTD4"    
## [11] "ISG20"      "LAG3"       "ODF3B"      "PDZD4"      "TMEM127"   
## [16] "TRAC"       "VTI1A"      "ZCCHC2"    
## [1] "found 17 genes."

## [1] 18
##  [1] "AHCTF1"   "CAPN15"   "CCDC112"  "DOPEY2"   "H6PD"     "HLA-DPB1"
##  [7] "HLA-DQA1" "KLHDC4"   "N4BP1"    "PNPLA6"   "PREX1"    "PTGDS"   
## [13] "RREB1"    "SLC38A10" "TBC1D9B"  "ZNF292"   "ZNF318"  
## [1] "found 17 genes."

## [1] 19
##  [1] "C12orf45" "CLDND1"   "CXXC5"    "GSTM1"    "ITGAE"    "KCTD7"   
##  [7] "KLRK1"    "MSC"      "NCR1"     "PAPSS1"   "RHOC"     "SESN1"   
## [13] "ARAP2"    "GALNT3"   "HIVEP3"   "NLRC3"    "SLF2"     "ZDHHC5"  
## [1] "found 17 genes."

## [1] 20
##  [1] "HMBOX1"  "KIF9"    "ABCA7"   "ANKRD36" "AP3B1"   "AP3M2"   "ARHGEF9"
##  [8] "C2CD3"   "C5orf24" "GPHN"    "PIP4K2B" "RIPOR2"  "UVRAG"   "VPS18"  
## [15] "VPS39"   "WDR60"   "XPO6"    "ZBTB20"  "ZNF407" 
## [1] "found 19 genes."

## [1] 21
##  [1] "GADD45B"     "TRBV6-1"     "AKNA"        "DENND4B"     "FAM78A"     
##  [6] "GPR132"      "HPS4"        "MT2A"        "NBEAL2"      "NUTM2B-AS1" 
## [11] "PCNX1"       "PUM3"        "SEC14L1"     "SLC16A1-AS1" "TRANK1"     
## [16] "TRBV2"       "TRGV4"       "TTC38"       "ZNF83"      
## [1] "found 17 genes."

## [1] 22
##  [1] "AC044849.1" "APMAP"      "C10orf91"   "MATK"       "BICRAL"    
##  [6] "ERBIN"      "GZMB"       "ITGAL"      "KIAA2026"   "MYO1G"     
## [11] "NKG7"       "RAP1GAP2"   "RASGRP1"    "RNF125"     "RNF19A"    
## [16] "SPON2"      "SRGN"       "VPS13C"    
## [1] "found 16 genes."

## [1] 23
##  [1] "AMD1"     "CCNL1"    "GLTP"     "NT5DC1"   "RGCC"     "RSRP1"   
##  [7] "SERINC5"  "SNHG12"   "ANKRD36B" "ANKRD36C" "CHD9"     "EML4"    
## [13] "ENOSF1"   "NFATC3"   "PARP4"    "SLFN12L"  "TEP1"     "TTC14"   
## [19] "ZNF708"  
## [1] "found 18 genes."

## [1] 24
##  [1] "AC008555.5" "AL135791.1" "BTG2"       "CXorf40A"   "LIME1"     
##  [6] "LINC00402"  "MCUB"       "PDCD4-AS1"  "PGGHG"      "PRAG1"     
## [11] "TNFRSF25"   "TRAV14DV4"  "ZNF749"     "CARD16"     "GK5"       
## [16] "MIAT"       "PCSK7"      "SPATA13"   
## [1] "found 12 genes."

## [1] 25
##  [1] "CSRNP1"  "ID1"     "TXK"     "ZC3H12A" "ARID5B"  "CISH"    "EHBP1L1"
##  [8] "FGL2"    "GBP1"    "GBP5"    "KLF6"    "MKL1"    "NFKBIZ"  "PIM1"   
## [15] "PLAC8"   "RIC3"    "SETD5"  
## [1] "found 17 genes."

## [1] 26
##  [1] "ABR"      "ARAP1"    "C16orf72" "CHD6"     "CREBZF"   "DUS1L"   
##  [7] "FAM53B"   "HECA"     "HERC3"    "HERC6"    "INPP5D"   "LY6E"    
## [13] "PARP11"   "RAB27B"   "SYTL3"    "TTC16"    "XAF1"     "ZNF652"  
## [1] "found 17 genes."

## [1] 27
##  [1] "CD27"     "CD28"     "COA1"     "COQ8A"    "CRLF3"    "CYB561A3"
##  [7] "GZMK"     "IER3"     "KLRG1"    "LEPROTL1" "RCSD1"    "RTRAF"   
## [13] "SLC38A1"  "STK17A"   "TMEM107"  "TMEM42"   "ZFAND1"   "RFWD3"   
## [1] "found 18 genes."

## [1] 28
##  [1] "AIF1"      "ANXA2R"    "BEX4"      "CHRM3-AS2" "EPS8"      "RCAN3"    
##  [7] "SELL"      "TCEA3"     "CASP10"    "CHD1"      "CYTH1"     "MIDN"     
## [13] "MSI2"      "RNF157"    "SCRN3"     "SOS1"      "VCAN"     
## [1] "found 16 genes."

## [1] 29
##  [1] "AOAH"     "CARHSP1"  "EOMES"    "GIMAP1"   "GSTM4"    "ADGRG1"  
##  [7] "DGKD"     "IGKV3-15" "IRF9"     "ITGAM"    "KIR2DL3"  "MYO1F"   
## [13] "NCKAP1L"  "NECAP1"   "PRKCH"    "SLFN5"    "TUT7"     "YPEL1"   
## [1] "found 18 genes."

## [1] 30
##  [1] "AC007384.1" "AC015982.1" "CCL4L2"     "MZF1-AS1"   "RETREG1"   
##  [6] "ABCC10"     "AC092683.1" "AP005482.1" "BMT2"       "FAM133B"   
## [11] "GRK2"       "MINDY2"     "POLR2J3-1"  "SIDT1"      "THAP5"     
## [16] "TRDC"       "TRDV1"      "XCL2"       "ZNF808"    
## [1] "found 13 genes."

## [1] 31
##  [1] "AC004687.1" "AC007952.4" "AC025164.1" "AC025171.3" "AC087239.1"
##  [6] "AC245014.3" "AL121944.1" "AL139246.5" "CRTAM"      "ILF3-DT"   
## [11] "JAML"       "NR4A3"      "SNHG8"      "SNHG9"      "TRAV12-2"  
## [16] "TRBV3-1"    "TRBV6-2"    "TRBV7-9"   
## [1] "found 7 genes."

## [1] 32
##  [1] "ADCY7"    "BCL9L"    "CELF2"    "CHST12"   "ETNK1"    "GALNT2"  
##  [7] "KCNAB2"   "KIAA1109" "KIAA1551" "KLF2"     "MPPE1"    "PLEK"    
## [13] "PRDM2"    "PTPN7"    "SUSD1"    "UGGT1"    "WDTC1"    "ZBP1"    
## [1] "found 17 genes."

## [1] 33
##  [1] "CD84"        "CMC1"        "FAM118A"     "GLA"         "HIKESHI"    
##  [6] "HLA-DMB"     "KIR3DL2"     "KLRC3"       "LETMD1"      "MAPRE2"     
## [11] "SH2D1A"      "TRAV38-2DV8" "TRBV6-5"     "TRGV9"       "MCOLN2"     
## [16] "TMEM181"    
## [1] "found 16 genes."

## [1] 34
##  [1] "GATA3"    "GPR183"   "MAP3K8"   "NR4A2"    "SLC4A4"   "TIGIT"   
##  [7] "ARHGAP10" "CSNK1G2"  "FAM160B1" "GPRIN3"   "LPCAT1"   "LRRC8A"  
## [13] "PARP14"   "RAPGEF1"  "SLC20A1"  "TBX21"    "TGFBR3"   "ZFAND3"  
## [1] "found 17 genes."

## [1] 35
##  [1] "ALKBH7"  "ARL4A"   "ATP5F1A" "C6orf48" "EFCAB2"  "FAM173A" "FCMR"   
##  [8] "MPST"    "NOSIP"   "PTRHD1"  "RGS10"   "ELMO1"   "IQGAP2"  "LPIN1"  
## [15] "PDE4B"   "PDE4D"   "TOB1"    "TUT4"   
## [1] "found 17 genes."

## [1] 36
##  [1] "AC012645.3" "AC016405.3" "AC020911.2" "AC083880.1" "AC091271.1"
##  [6] "AC103591.3" "AF213884.3" "AL357060.1" "ARF4-AS1"   "C6orf99"   
## [11] "CSKMT"      "HIPK1-AS1"  "INTS6L"     "KCNQ1OT1"   "LINC01465" 
## [16] "NPIPB4"     "OSER1-DT"   "Z93241.1"  
## [1] "found 3 genes."

## [1] 37
##  [1] "BNIP3L"  "MXI1"    "NUAK2"   "PDE3B"   "GALNT10" "HIPK1"   "IFI44L" 
##  [8] "MBD5"    "NRDC"    "PPM1K"   "RASA3"   "RLF"     "SETX"    "TMEM8A" 
## [15] "TRBV7-6" "VPS13B"  "VPS13D" 
## [1] "found 17 genes."

## [1] 38
##  [1] "AL138963.3" "IGLV1-44"   "LRRN3"      "LST1"       "MATR3-1"   
##  [6] "NOCT"       "THAP9-AS1"  "TRAV1-2"    "TRAV21"     "TRAV5"     
## [11] "TRAV8-4"    "TRBV20-1"   "TRBV28"     "TRBV9"      "TRGV7"     
## [16] "VAMP7"      "IFI27"     
## [1] "found 13 genes."

## [1] 39
##  [1] "C12orf10"     "COQ7"         "CXorf57"      "EPB41L4A-AS1" "FAM102A"     
##  [6] "HIST1H3H"     "IFRD1"        "LDLRAP1"      "LTB"          "NELL2"       
## [11] "TCF7"         "TMEM204"      "ZNF10"        "ZNF575"       "MAPK8IP3"    
## [16] "USP34"        "ZBTB40"      
## [1] "found 15 genes."

## [1] 40
##  [1] "AL136454.1" "BX284668.6" "TRAV8-2"    "DDX3Y"      "EIF1AY"    
##  [6] "ETFDH"      "KDM5D"      "MAF"        "MTERF2"     "RPAP1"     
## [11] "RPS4Y1"     "SBNO2"      "TRAV17"     "TTTY15"     "UTY"       
## [16] "ZMIZ2"      "ZNF236"    
## [1] "found 14 genes."

Session information

gc()
##            used  (Mb) gc trigger  (Mb) limit (Mb) max used  (Mb)
## Ncells  4179730 223.3   11673970 623.5         NA 11673970 623.5
## Vcells 20591749 157.2   61723001 471.0      65536 61693859 470.7
sessionInfo()
## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] stringr_1.5.0     limma_3.54.2      tidyr_1.3.0       ggpubr_0.6.0     
## [5] ggplot2_3.4.2     data.table_1.14.8
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.10            png_0.1-8              Biostrings_2.66.0     
##  [4] digest_0.6.31          utf8_1.2.3             R6_2.5.1              
##  [7] GenomeInfoDb_1.34.9    backports_1.4.1        stats4_4.2.3          
## [10] RSQLite_2.3.1          evaluate_0.20          httr_1.4.6            
## [13] pillar_1.9.0           zlibbioc_1.44.0        rlang_1.1.0           
## [16] rstudioapi_0.14        car_3.1-2              jquerylib_0.1.4       
## [19] blob_1.2.4             R.oo_1.25.0            R.utils_2.12.2        
## [22] S4Vectors_0.36.2       rmarkdown_2.21         labeling_0.4.2        
## [25] RCurl_1.98-1.12        bit_4.0.5              munsell_0.5.0         
## [28] broom_1.0.4            compiler_4.2.3         xfun_0.39             
## [31] pkgconfig_2.0.3        BiocGenerics_0.44.0    htmltools_0.5.5       
## [34] tidyselect_1.2.0       KEGGREST_1.38.0        GenomeInfoDbData_1.2.9
## [37] tibble_3.2.1           IRanges_2.32.0         fansi_1.0.4           
## [40] crayon_1.5.2           dplyr_1.1.2            withr_2.5.0           
## [43] R.methodsS3_1.8.2      bitops_1.0-7           grid_4.2.3            
## [46] jsonlite_1.8.4         gtable_0.3.3           lifecycle_1.0.3       
## [49] DBI_1.1.3              magrittr_2.0.3         scales_1.2.1          
## [52] cli_3.6.1              stringi_1.7.12         cachem_1.0.7          
## [55] carData_3.0-5          farver_2.1.1           XVector_0.38.0        
## [58] ggsignif_0.6.4         bslib_0.4.2            generics_0.1.3        
## [61] vctrs_0.6.2            RColorBrewer_1.1-3     org.Hs.eg.db_3.16.0   
## [64] tools_4.2.3            bit64_4.0.5            Biobase_2.58.0        
## [67] glue_1.6.2             purrr_1.0.1            abind_1.4-5           
## [70] fastmap_1.1.1          yaml_2.3.7             AnnotationDbi_1.60.2  
## [73] colorspace_2.1-0       rstatix_0.7.2          memoise_2.0.1         
## [76] knitr_1.44             sass_0.4.5